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   &#160;<span id="projectnumber">2.x</span>
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<div class="header">
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<div class="title">TreeBuilderManager Member List</div>  </div>
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<p>This is the complete list of members for <a class="el" href="class_tree_builder_manager.html">TreeBuilderManager</a>, including all inherited members.</p>
<table class="directory">
  <tr class="even"><td class="entry"><a class="el" href="class_tree_builder_manager.html#af1e010b6d69ec4c8a7860041ba823b68a5496170f117c3d558853e10ccee02666">alignment</a> enum value</td><td class="entry"><a class="el" href="class_tree_builder_manager.html">TreeBuilderManager</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_tree_builder_manager.html#ae26c0058859fbe67055a43f55b7c5008">AlphabetType</a> enum name</td><td class="entry"><a class="el" href="class_tree_builder_manager.html">TreeBuilderManager</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_tree_builder_manager.html#a3047ef12674cd2feab230d5445ec057e">alphType</a></td><td class="entry"><a class="el" href="class_tree_builder_manager.html">TreeBuilderManager</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_tree_builder_manager.html#ae26c0058859fbe67055a43f55b7c5008a089be0a828fca4605323da2e3a171202">amino</a> enum value</td><td class="entry"><a class="el" href="class_tree_builder_manager.html">TreeBuilderManager</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_tree_builder_manager.html#a150db90e2abf2fc03731688eb898bbb3">chars</a></td><td class="entry"><a class="el" href="class_tree_builder_manager.html">TreeBuilderManager</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_tree_builder_manager.html#a373cf550fdc215fc25daf72e40b56a8d">CorrectionType</a> enum name</td><td class="entry"><a class="el" href="class_tree_builder_manager.html">TreeBuilderManager</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_tree_builder_manager.html#adf86247bbac061e015008cf779aa1922">corrType</a></td><td class="entry"><a class="el" href="class_tree_builder_manager.html">TreeBuilderManager</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_tree_builder_manager.html#a4cd821248549c591777002b96d1b1f17a19cba20113304d5be5b0b1b3cdb11b91">dist</a> enum value</td><td class="entry"><a class="el" href="class_tree_builder_manager.html">TreeBuilderManager</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_tree_builder_manager.html#af1e010b6d69ec4c8a7860041ba823b68a6d9503e62c1cc7af8faafe95ca03fa9f">distance</a> enum value</td><td class="entry"><a class="el" href="class_tree_builder_manager.html">TreeBuilderManager</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_tree_builder_manager.html#ae26c0058859fbe67055a43f55b7c5008a9cf0eb2046097228c5269e9da5e47cba">dna</a> enum value</td><td class="entry"><a class="el" href="class_tree_builder_manager.html">TreeBuilderManager</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_tree_builder_manager.html#a82bd45375c241cc86bf5d26f4fef05ed">doJob</a>()</td><td class="entry"><a class="el" href="class_tree_builder_manager.html">TreeBuilderManager</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_tree_builder_manager.html#a373cf550fdc215fc25daf72e40b56a8da7bff75f1893babce718611848369ad04">FastTree</a> enum value</td><td class="entry"><a class="el" href="class_tree_builder_manager.html">TreeBuilderManager</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_tree_builder_manager.html#ac2e2786055dddad38c1bdce4087638e8">inFile</a></td><td class="entry"><a class="el" href="class_tree_builder_manager.html">TreeBuilderManager</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_tree_builder_manager.html#af1e010b6d69ec4c8a7860041ba823b68">InputType</a> enum name</td><td class="entry"><a class="el" href="class_tree_builder_manager.html">TreeBuilderManager</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_tree_builder_manager.html#aae28e02c9576d10f1d060a9b35e948d9">inType</a></td><td class="entry"><a class="el" href="class_tree_builder_manager.html">TreeBuilderManager</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_tree_builder_manager.html#a373cf550fdc215fc25daf72e40b56a8da78e91f6ce40102b0d61e8b9d51750638">JukesCantor</a> enum value</td><td class="entry"><a class="el" href="class_tree_builder_manager.html">TreeBuilderManager</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_tree_builder_manager.html#a373cf550fdc215fc25daf72e40b56a8dae1e7c68b84de2d982d8fc029b480cc17">Kimura2</a> enum value</td><td class="entry"><a class="el" href="class_tree_builder_manager.html">TreeBuilderManager</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_tree_builder_manager.html#a4c1a65ed414d8317911abe3d4f704bf6">method</a></td><td class="entry"><a class="el" href="class_tree_builder_manager.html">TreeBuilderManager</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_tree_builder_manager.html#a5710efedbd3702d1dc95d0722e757351">names</a></td><td class="entry"><a class="el" href="class_tree_builder_manager.html">TreeBuilderManager</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_tree_builder_manager.html#a4c60ce04a47c306072401de1d9d83571">newDistanceMethod</a></td><td class="entry"><a class="el" href="class_tree_builder_manager.html">TreeBuilderManager</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_tree_builder_manager.html#a7e62c0d18ca2e9782f6e1f689b4388d4">njTmpDir</a></td><td class="entry"><a class="el" href="class_tree_builder_manager.html">TreeBuilderManager</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_tree_builder_manager.html#a373cf550fdc215fc25daf72e40b56a8daa48e32132856572cccb189cd72e521c7">none</a> enum value</td><td class="entry"><a class="el" href="class_tree_builder_manager.html">TreeBuilderManager</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_tree_builder_manager.html#a373cf550fdc215fc25daf72e40b56a8da6a180df7a39a3dd2e0f2283fbdc9c9eb">not_assigned</a> enum value</td><td class="entry"><a class="el" href="class_tree_builder_manager.html">TreeBuilderManager</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_tree_builder_manager.html#ae26c0058859fbe67055a43f55b7c5008a229d43ec692cb711e87fa15d1a163c4a">null</a> enum value</td><td class="entry"><a class="el" href="class_tree_builder_manager.html">TreeBuilderManager</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_tree_builder_manager.html#a9ae531e04f5efb9fe8228ede332404dd">NUM_RAND_DIR_CHARS</a></td><td class="entry"><a class="el" href="class_tree_builder_manager.html">TreeBuilderManager</a></td><td class="entry"><span class="mlabel">static</span></td></tr>
  <tr><td class="entry"><a class="el" href="class_tree_builder_manager.html#a0efd9a961ff0dd21dc150202ad0dab65">outFile</a></td><td class="entry"><a class="el" href="class_tree_builder_manager.html">TreeBuilderManager</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_tree_builder_manager.html#a4cd821248549c591777002b96d1b1f17">OutputType</a> enum name</td><td class="entry"><a class="el" href="class_tree_builder_manager.html">TreeBuilderManager</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_tree_builder_manager.html#abdf50c04e7fbf7355186615c94738940">outType</a></td><td class="entry"><a class="el" href="class_tree_builder_manager.html">TreeBuilderManager</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_tree_builder_manager.html#ac022773150741a88a56920d768b366d4">threads</a></td><td class="entry"><a class="el" href="class_tree_builder_manager.html">TreeBuilderManager</a></td><td class="entry"></td></tr>
  <tr><td class="entry"><a class="el" href="class_tree_builder_manager.html#a4cd821248549c591777002b96d1b1f17a432f48fbf28ef0573a1a3848b5cf1d40">tree</a> enum value</td><td class="entry"><a class="el" href="class_tree_builder_manager.html">TreeBuilderManager</a></td><td class="entry"></td></tr>
  <tr class="even"><td class="entry"><a class="el" href="class_tree_builder_manager.html#a1c1e9bc07025dd5160ac37277c10647a">TreeBuilderManager</a>(std::string method, std::string njTmpDir, std::string inFile, FILE *outfile, InputType inType, OutputType outType, AlphabetType alphType, CorrectionType corrType, int threads, bool useSSE)</td><td class="entry"><a class="el" href="class_tree_builder_manager.html">TreeBuilderManager</a></td><td class="entry"></td></tr>
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